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Alternative splicing (AS) is an important mechanism of gene regulation that contributes to protein diversity. It is of great significance to recognize different kinds of AS accurately so as to understand the mechanism of gene regulation. Many in silico methods have been applied to detecting AS with vast features, but the result is far from satisfactory. In this paper, we used the features proven to be useful in recognizing AS in previous literature and proposed a hybrid method combining Gene Expression Programming (GEP) and Random Forests (RF) to classify the constitutive exons and cassette exons which is the most common AS phenomenon. GEP will firstly make prediction to the samples of strong signal, and the other samples of weak signal will be distinguished with a more complex classifier based on RF. The experiment result indicates that this method can highly improve the recognition level in this issue. [ABSTRACT FROM AUTHOR]

Abstract: A triticale cDNA encoding a prolyl aminopeptidase (PAP) was obtained by RT-PCR and has been designated as TsPAP1. The cloned cDNA is 1387bp long and encodes a protein of 390 amino acids with a calculated molecular mass of 43.9kDa. The deduced TsPAP1 protein exhibits a considerable sequence identity with the biochemically characterized bacterial and fungal PAP proteins of small molecular masses (∼35kDa). Moreover, the presence of conserved regions that are characteristic for bacterial monomeric PAP enzymes (the GGSWG motif, the localization of the catalytic triad residues and the segment involved in substrate binding) has also been noted. Primary structure analysis and phylogenetic analysis revealed that TsPAP1 encodes a novel plant PAP protein that is distinct from the multimeric proteins that have thus far been characterized in plants and whose counterparts have been recognized only in bacteria and fungi. A significant increase in the TsPAP1 transcript level in the shoots of triticale plants was observed under drought and saline conditions as well as in the presence of cadmium and aluminium ions in the nutrient medium. This paper is the first report describing changes in the transcript levels of any plant PAP in response to suboptimal growth conditions. [Copyright &y& Elsevier]

The protein-tyrosine kinase p56lck is the product of the lck gene. It plays a pivotal role in T-lymphocyte activation and thymocyte development, as indicated by the defective immune responses of lck−/− mice. We have demonstrated that an exon 7-deleted lck mRNA is produced by alternative splicing in all human cells expressing the lck gene. We have now looked for the protein encoded by this spliced lck mRNA and attempted to determine the function of the deleted Lck protein. This paper shows that the LckΔ7 protein is present in JCaM1.6 T-cells and we inferred that this isoform accounts for 15% of the total Lck proteins in the parental Jurkat T-cell line. We report that deletion of the first 51 amino-acids (exon 7) of the Lck catalytic domain greatly reduces the kinase activity of the recombinant protein. The residual activity can, nevertheless, be enhanced by adding Mn2+, whereas this cation has no effect on the activity of the p56lck mutated in its active site (K273E). The enforced production of LckΔ7 protein in transfected Jurkat cells results in slower cell proliferation than does p56lck. These findings suggest that the LckΔ7 protein is a p56lck cell-signaling regulator. This mechanism could be common to both humans and mice, in which we also found the exon 7-spliced lck transcript. [Copyright &y& Elsevier]